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- PDB-3ckr: Crystal structure of BACE-1 in complex with inhibitor -

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Basic information

Entry
Database: PDB / ID: 3ckr
TitleCrystal structure of BACE-1 in complex with inhibitor
ComponentsBeta-secretase 1
KeywordsHYDROLASE / beta-secretase / aspartyl protease / Alternative splicing / Glycoprotein / Membrane / Transmembrane / Zymogen
Function / homology
Function and homology information


memapsin 2 / Golgi-associated vesicle lumen / signaling receptor ligand precursor processing / beta-aspartyl-peptidase activity / amyloid precursor protein catabolic process / amyloid-beta formation / membrane protein ectodomain proteolysis / cellular response to manganese ion / amyloid-beta metabolic process / prepulse inhibition ...memapsin 2 / Golgi-associated vesicle lumen / signaling receptor ligand precursor processing / beta-aspartyl-peptidase activity / amyloid precursor protein catabolic process / amyloid-beta formation / membrane protein ectodomain proteolysis / cellular response to manganese ion / amyloid-beta metabolic process / prepulse inhibition / detection of mechanical stimulus involved in sensory perception of pain / cellular response to copper ion / presynaptic modulation of chemical synaptic transmission / hippocampal mossy fiber to CA3 synapse / multivesicular body / response to lead ion / trans-Golgi network / recycling endosome / protein processing / cellular response to amyloid-beta / positive regulation of neuron apoptotic process / synaptic vesicle / late endosome / peptidase activity / amyloid-beta binding / endopeptidase activity / amyloid fibril formation / lysosome / aspartic-type endopeptidase activity / early endosome / endosome membrane / endosome / membrane raft / Amyloid fiber formation / endoplasmic reticulum lumen / axon / neuronal cell body / dendrite / Golgi apparatus / enzyme binding / cell surface / proteolysis / membrane / plasma membrane
Similarity search - Function
Beta-secretase BACE1 / Beta-secretase BACE / Memapsin-like / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site ...Beta-secretase BACE1 / Beta-secretase BACE / Memapsin-like / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-009 / Beta-secretase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsMin, K.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2008
Title: Synthesis, SAR, and X-ray structure of human BACE-1 inhibitors with cyclic urea derivatives
Authors: Park, H. / Min, K. / Kwak, H.-S. / Koo, K.D. / Lim, D. / Seo, S.-W. / Choi, J.-U. / Platt, B. / Choi, D.-Y.
History
DepositionMar 16, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 3, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-secretase 1
B: Beta-secretase 1
C: Beta-secretase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,5886
Polymers137,7713
Non-polymers1,8173
Water1,63991
1
A: Beta-secretase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5292
Polymers45,9241
Non-polymers6061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-secretase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5292
Polymers45,9241
Non-polymers6061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-secretase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5292
Polymers45,9241
Non-polymers6061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)224.457, 108.126, 61.135
Angle α, β, γ (deg.)90.000, 100.870, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Beta-secretase 1 / / Beta-site APP cleaving enzyme 1 / Beta-site amyloid precursor protein cleaving enzyme 1 / Membrane- ...Beta-site APP cleaving enzyme 1 / Beta-site amyloid precursor protein cleaving enzyme 1 / Membrane-associated aspartic protease 2 / Memapsin-2 / Aspartyl protease 2 / Asp 2 / ASP2


Mass: 45923.547 Da / Num. of mol.: 3 / Fragment: protease domain, UNP residues 43-454 / Mutation: R-6K, R-5K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P56817, memapsin 2
#2: Chemical ChemComp-009 / (4S)-1,4-dibenzyl-N-[(1S,2R)-1-benzyl-3-{[3-(dimethylamino)benzyl]amino}-2-hydroxypropyl]-2-oxoimidazolidine-4-carboxamide


Mass: 605.769 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C37H43N5O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.48 %
Crystal growMethod: vapor diffusion, sitting drop / Details: vapor diffusion, sitting drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. all: 39081 / Num. obs: 35675 / % possible obs: 91.5 % / Rmerge(I) obs: 0.148 / Χ2: 1.091 / Net I/σ(I): 4.2
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
2.7-2.80.39125850.47166.3
2.8-2.910.33928450.50673.5
2.91-3.040.332720.57184.6
3.04-3.20.25736250.61893.1
3.2-3.40.22638160.78998.5
3.4-3.660.18438841.0999.9
3.66-4.030.15938911.354100
4.03-4.60.13139071.59199.8
4.6-5.770.12538851.60899.8
5.77-200.09739651.61699.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
PDB_EXTRACT3.004data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→19.96 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 44929.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1661 5 %RANDOM
Rwork0.251 ---
obs-34842 84.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 22.48 Å2 / ksol: 0.272 e/Å3
Displacement parametersBiso mean: 52.2 Å2
Baniso -1Baniso -2Baniso -3
1--28.46 Å20 Å2-7.26 Å2
2---12.35 Å20 Å2
3---40.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.44 Å
Luzzati d res low-5 Å
Luzzati sigma a0.62 Å0.67 Å
Refinement stepCycle: LAST / Resolution: 2.7→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8909 0 135 91 9135
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.6
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.407 176 4.9 %
Rwork0.374 3404 -
all-3580 -
obs--55.1 %

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